Mercurial > repos > jjohnson > bamtools_split
changeset 1:59f09c61031c draft default tip
Deleted selected files
| author | jjohnson |
|---|---|
| date | Mon, 15 May 2017 16:44:31 -0400 |
| parents | 8c17ddca0eee |
| children | |
| files | ._bamtools-split-ref.xml ._bamtools-split-tag.xml bamtools-split.xml.save |
| diffstat | 3 files changed, 0 insertions(+), 146 deletions(-) [+] |
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--- a/bamtools-split.xml.save Mon May 15 16:27:18 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,146 +0,0 @@ -<tool id="bamSplit" name="Split" version="2.4.1"> - <description>BAM datasets on variety of attributes</description> - <macros> - <xml name="macro_output_type"> - <param name="output_type" type="select" label="output as"> - <option value="history_items">history items</option> - <option value="dataset_collection">dataset_collection</option> - </param> - </xml> - </macros> - <requirements> - <requirement type="package" version="2.4.0">bamtools</requirement> - </requirements> - <command> - <![CDATA[ - echo "BAM" > $report && - #for $bam_count, $input_bam in enumerate( $input_bams ): - ln -s "${input_bam}" "localbam_${bam_count}.bam" && - ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && - #end for - bamtools - split - #if str ( $analysis_type.analysis_type_selector ) == "-tag" : - ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}" - #else - ${analysis_type.analysis_type_selector} - #end if - -stub split_bam - #for $bam_count, $input_bam in enumerate( $input_bams ): - -in "localbam_${bam_count}.bam" - #end for - #if str ( $analysis_type.analysis_type_selector ) == "-reference" and $analysis_type.output_type == "dataset_collection": - #import re - #set $name = $re.sub('\W','_',$re.sub('\.bam$','',$input_bams[0].name)) - #set $ref_list = ' '.join([$re.sub('^.*__sq__(.+)__sq__.*$','\\1',n) if n.find('__sq__') >= 0 else n for n in str($input_bam.metadata.reference_names).split(',')]) - && (export I=0; - for i in $ref_list; - do I=\$((++I)); SN=`printf "split_bam.REF_%s.bam" "\$i"`; - if [ -e \$SN ]; - then FN=`printf "split_bam%05d%s.%s.bam" \$((I)) "$name" "\$i"`; - mv \$SN \$FN; - fi; - done) - #end if - ]]> - </command> - <inputs> - <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/> - <conditional name="analysis_type"> - <param name="analysis_type_selector" type="select" label="Split BAM dataset(s) by" help="See help below for explanation of each option"> - <option value="-mapped">Mapping status (-mapped)</option> - <option value="-paired">Pairing status (-paired)</option> - <option value="-reference">Reference name (-reference)</option> - <option value="-tag">Specific tag (-tag)</option> - </param> - <when value="-mapped" /> - <when value="-paired" /> - <when value="-reference" > - <expand macro="macro_output_type" /> - </when> - <when value="-tag"> - <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter "NM""/> - <expand macro="macro_output_type" /> - </when> - </conditional> - </inputs> - <outputs> - <data format="txt" name="report" label="BAMSplitter Run" hidden="true"> - <discover_datasets pattern="split_bam\.(?P<designation>.+)\.bam" ext="bam" visible="true"/> - <filter>analysis_type['analysis_type_selector'] in ('-mapped','-paired') or analysis_type['output_type'] != 'dataset_collection'</filter> - </data> - <collection name="output_bams" type="list" label="${input_bams[0].name} by ${analysis_type.analysis_type_selector.replace('-','')}"> - <discover_datasets pattern="split_bam\d*(?P<designation>.+)\.bam" ext="bam" visible="false"/> - <filter>analysis_type['analysis_type_selector'] in ('-reference','-tag') and analysis_type['output_type'] == 'dataset_collection'</filter> - </collection> - </outputs> - <tests> - <test> - <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> - <param name="analysis_type_selector" value="-mapped"/> - <output name="report"> - <assert_contents> - <has_line line="BAM" /> - </assert_contents> - <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/> - </output> - </test> - <test> - <param name="input_bams" ftype="bam" value="bamtools-input2.bam"/> - <param name="analysis_type_selector" value="-reference"/> - <param name="output_type" value="dataset_collection"/> - <output_collection name="output_bams" type="list"> - <element name="bamtools_input2.chr1" file="bamtools_input2.chr1" compare="sim_size" delta="500" /> - </output_collection> - </test> - - </tests> - <help> -**What is does** - -BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools). - ------ - -.. class:: warningmark - -**DANGER: Multiple Outputs** - -As described below, splitting a BAM dataset(s) on reference name or a tag value can produce very large numbers of outputs. Read below and know what you are doing. - ------ - -**How it works** - -The following options can be specified via "**Split BAM dataset(s) by**" dropdown:: - - Mapping status (-mapped) split mapped/unmapped and generate two output files - named (MAPPED) and (UNMAPPED) containing mapped and unmapped - reads, respectively. - - Pairing status (-paired) split single-end/paired-end alignments and generate two output files - named (SINGLE_END) and (PAIRED_END) containing paired and unpaired - reads, respectively. - - Reference name (-reference) split alignments by reference name. In cases of unfinished genomes with - very large number of reference sequences (scaffolds) it can generate - thousands (if not millions) of output datasets. - - Specific tag (-tag) split alignments based on all values of TAG encountered. Choosing this - option from the menu will allow you to enter the tag name. As was the - case with the reference splitting above, this option can produce very - large number of outputs if a tag has a large number of unique values. - ------ - -.. class:: infomark - -**More information** - -Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki - - </help> - <citations> - <citation type="doi">10.1093/bioinformatics/btr174</citation> - </citations> -</tool>